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OpenMM testbed for constant-pH methodologies.

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choderalab/protons

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Testbed for constant-pH methodologies using OpenMM.

Manifest

protons/ - Python module implementing constant-pH methodologies in Python

   calibration.py        - Calibration engines   cnstphgbforces.py     - CustomGBForces that exclude contributions from discharged protons   ligutils.py           - Work in progress code for ligand parametrization.   tests/                - Unit tests

protons/examples/

   explicit-solvent-example.py - explicit solvent NCMC example   amber-example/        - example system set up with AmberTools constant-pH tools   calibration-implicit/ - terminally-blocked amino acids parameterized for implicit solvent relative free energy calculations   calibration-explicit/ - terminally-blocked amino acids parameterized for explicit solvent relative free energy calculations

references/ - some relevant literature references

Dependencies

protons will eventually be made conda installable. The list of dependencies can be foundhere.

Contributors / coauthors


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